Currently, my program unmarshals the Network object successfully, but there's no connection between Network and NetworkInputs that allows JAXB to "see" the nodes that exist in Network. I want my Flow objects to point to the correct Node in the Network class.

Where the resolver could be used over many inststance of the unmarshaller.
But the point is that the resolver will not clear itsself on startDocument as the default implementation of com.sun.xml.internal.bind.v2.runtime.unmarshaller.DefaultIDResolver does: